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How much information is 473 genes? How many bytes does this represent, in a compact but "raw" encoding? What about if you compressed it with gzip? Also what

How much information is 473 genes? How many bytes does this represent, in a compact but "raw" encoding? What about if you compressed it with gzip? Also what are the raw/compressed sizes for a human genome? I have wondered this for a long time but never seem to find a concrete answer.

gberger 10y ago
From [1], "Mycoplasma genitalium: it has only about 480 genes in its genome of 580 070 nucleotide pairs." So in average, each gene is 1200 nucleotide pairs. A nucleotide is one of [A,T,C,G]. So that means it encodes 2 bits of information. 473 * 1200 * 2 = 1 135 200 bits, or 141.9 kilobyte. Of course, this is coming from a software developer using numbers from Google, so I might be wildly wrong. [1] "Molecular biology of the cell" by Bruce Alberts
- haberman 10y ago
  That's a great start at least! Posting something that is wildly wrong is the best way to get someone who knows more to interject with corrected information, so hopefully someone with expertise can confirm or deny.
  - gberger 10y ago
    Cunningham's Law
- pYQAJ6Zm 10y ago
  141.9 kB! In the future, I expect there will be a demoscene of biosynthetics.
amphitoky 10y ago
the cellular genome size of RGD3.0, the organism with a 473 genome, is 531kbp according to the paper. this means that the genome encompasses ~531,000 nucleotides (base-pairs). for reference, the human genome encompasses approximately 3.3-billion base-pairs. you can download the human genome from here http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.... (it is recommended to use ftp, see: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/ http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/). it is an ~800mb download. if it takes 800 mb to store 3.3 billion bases, i would assume it takes (531k / 3.3b) * 800 mb = 0.141 mb to store this genome.
- haberman 10y ago
  Thanks! By the way, when you say "you can download the human genome", presumably this is the genome of a specific individual whose DNA was sequenced? What person is that?
  - amphitoky 10y ago
    no, it is a consensus sequence determined by sequencing the genomes of several individuals. i do not know how many individuals were sequenced for hg38, but hg37 was derived from 13 individuals according to [1]. genomic regions with higher variability between individuals are annotated separately and are not represented in the main chromosomal sequence, but can be aligned to it as such. [1] https://en.wikipedia.org/wiki/Reference_genome https://en.wikipedia.org/wiki/Reference_genome
  - ealloc 10y ago
    You can download Craig Venter's genome here: http://hgdownload.soe.ucsc.edu/goldenPath/venter1/bigZips/ http://hgdownload.soe.ucsc.edu/goldenPath/venter1/bigZips/ However, the human "reference" genome (the updated main product of the Human Genome Project) is a patchwork of about 20 donors' genomes. Many(most?) of the donors are anonymous volunteers from Buffalo, NY, USA. http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/ http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/

gberger 10y ago

From [1], "Mycoplasma genitalium: it has only about 480 genes in its genome of 580 070 nucleotide pairs." So in average, each gene is 1200 nucleotide pairs. A nucleotide is one of [A,T,C,G]. So that means it encodes 2 bits of information. 473 * 1200 * 2 = 1 135 200 bits, or 141.9 kilobyte. Of course, this is coming from a software developer using numbers from Google, so I might be wildly wrong. [1] "Molecular biology of the cell" by Bruce Alberts

haberman 10y ago
That's a great start at least! Posting something that is wildly wrong is the best way to get someone who knows more to interject with corrected information, so hopefully someone with expertise can confirm or deny.
- gberger 10y ago
  Cunningham's Law
pYQAJ6Zm 10y ago
141.9 kB! In the future, I expect there will be a demoscene of biosynthetics.

amphitoky 10y ago

the cellular genome size of RGD3.0, the organism with a 473 genome, is 531kbp according to the paper. this means that the genome encompasses ~531,000 nucleotides (base-pairs). for reference, the human genome encompasses approximately 3.3-billion base-pairs. you can download the human genome from here http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.... (it is recommended to use ftp, see: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/ http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/). it is an ~800mb download. if it takes 800 mb to store 3.3 billion bases, i would assume it takes (531k / 3.3b) * 800 mb = 0.141 mb to store this genome.

haberman 10y ago
Thanks! By the way, when you say "you can download the human genome", presumably this is the genome of a specific individual whose DNA was sequenced? What person is that?
- amphitoky 10y ago
  no, it is a consensus sequence determined by sequencing the genomes of several individuals. i do not know how many individuals were sequenced for hg38, but hg37 was derived from 13 individuals according to [1]. genomic regions with higher variability between individuals are annotated separately and are not represented in the main chromosomal sequence, but can be aligned to it as such. [1] https://en.wikipedia.org/wiki/Reference_genome https://en.wikipedia.org/wiki/Reference_genome
- ealloc 10y ago
  You can download Craig Venter's genome here: http://hgdownload.soe.ucsc.edu/goldenPath/venter1/bigZips/ http://hgdownload.soe.ucsc.edu/goldenPath/venter1/bigZips/ However, the human "reference" genome (the updated main product of the Human Genome Project) is a patchwork of about 20 donors' genomes. Many(most?) of the donors are anonymous volunteers from Buffalo, NY, USA. http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/ http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/